Genomic diversity and the domestication history of cotton ( <i>Gossypium hirsutum</i> )
Abstract
Gossypium hirsutum is the leading fiber crop globally, but its origin as a domesticated plant and patterns of diversity in the wild remain to be elucidated. Here, we use extensive sampling of wild populations and comparative genome sequence data to illuminate the scope and patterning of wild cotton diversity across its native range. Analyses confirm the hypothesis that the Yucatán Peninsula (México) is the center of domestication, from which the original perennial forms and later modern annualized cultivars were derived. Population structure and phylogenomic analyses indicate that northwestern Yucatán harbors greater genetic diversity relative to smaller, geographically dispersed populations in northeastern Yucatán and the Caribbean basin. Genetic load and transposable element burden also are the lowest in northwestern Yucatán relative to other regions, consistent with its greater diversity and reflecting the effects of historical genetic bottlenecks in other populations. Populations from Florida and elsewhere in the Caribbean basin maintain unique pockets of diversity. Analyses of selection suggest that cotton domestication entailed long-term accumulation of mutations with relatively minor phenotypic effects, as opposed to a more punctuated process involving major domestication genes. Our study quantifies the scope and scale of genomic diversity in wild cotton, the origin of the cultivated gene pool, and the likely ecological and anthropogenic processes that shaped extant diversity and modern geographic patterning.
Article Details
Journal Info
Proceedings of the National Academy of Sciences
National Academy of Sciences
Authors (20)
Weixuan Ning
Department of Ecology, Evolution, and Organismal Biology, Iowa State University
Mark A. Arick
Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University
Joshua A. Udall
Crop Germplasm Research Unit, United States Department of Agriculture/Agricultural Research Service
Chuan-Yu Hsu
Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University
Luis Abdala-Roberts
Universidad Nacional Autónoma de México, Escuela Nacional de Estudios Superiores Unidad Mérida
Uriel Solís-Rodríguez
Departamento de Ecología Tropical, Campus de Ciencias Biológicas y Agropecuarias, Universidad Autónoma de Yucatán
Yeyson Briones-May
Departamento de Ecología Tropical, Campus de Ciencias Biológicas y Agropecuarias, Universidad Autónoma de Yucatán
Zenaida V. Magbanua
Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University
Olga Pechanova
Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University
Carlos Bustos-Segura
Institute of Biology, Fundamental and Applied Research in Chemical Ecology, University of Neuchâtel
Mary V. Clancy
Institute of Biology, Fundamental and Applied Research in Chemical Ecology, University of Neuchâtel
Sandra Díaz-Cruz
Departamento de Ecología Tropical, Campus de Ciencias Biológicas y Agropecuarias, Universidad Autónoma de Yucatán
Alejandra Garnica-Cabrera
Universidad Nacional Autónoma de México, Escuela Nacional de Estudios Superiores Unidad Mérida
Marine Mamin
Institute of Biology, Fundamental and Applied Research in Chemical Ecology, University of Neuchâtel
John Z. Yu
Crop Germplasm Research Unit, United States Department of Agriculture/Agricultural Research Service
Ted C. J. Turlings
Institute of Biology, Fundamental and Applied Research in Chemical Ecology, University of Neuchâtel
Guanjing Hu
National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences
Daniel G. Peterson
Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University
Corrinne E. Grover
Department of Ecology, Evolution, and Organismal Biology, Iowa State University
Jonathan F. Wendel
Department of Ecology, Evolution and Organismal Biology, Iowa State University